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What can I do when I have problems opening the 3D rollup, 3D Gel Image Regions or the 3D view of a PCA result?

The Problem

You are trying to open the 3D-view for a spot in the Dual View (Dual View Menu: Rollups -> 3D Spots), the 3D-view in Gel Image Regions View or for a PCA result, but one of the following happens:

The rollup opens, but is completely blank.

Before you begin to fix the problem of a blank 3D-rollup: Please make sure that the rollup does not correctly present a blank area of your gel image but really should display a spot by clicking somewhere in the Gel image randomly with the Spot Selection Tool of the Dualview.

Please note, that selecting several spots at once does not show the complete area in the 3D rollup, but simply does nothing with the 3D rollup. If you want to view a bigger area than a single spot in a 3D representation, open the Preferences > 3D Spots and check the mark on fixed size. In the nearby textbox you can set the size of area you want to be shown in pixels. Please mind, that the bigger this value is, the more time is needed for computing the representation. Now you can click in the desired area, select several spots and watch them in the 3D Rollup.

The Dual View suddenly disappears, or Delta2D crashes completely

The underlying Sun Java™ software has problems controlling the installed graphics interface, which can have multiple reasons:

  1. The graphics drivers installed on many computers are only the basic drivers offered by the used operating system and were never updated. These drivers mostly lack the advanced functions needed for a 3D-representation.

  2. To benefit from the ongoing development of Java, the Java components used in Delta2D are kept up to date. Sometimes it can happen that modifications of certain parts of Java are not or not yet compatible to all graphics drivers.

  3. Some computers are equipped with so called "on board graphics chipsets". This is not generally a bad idea, since it saves costs and they do most jobs very well. But sometimes such a chipset lacks abilities needed for 3D representation.

  4. Especially for older versions of Microsoft® Windows™ to increase performance users have been advised to modify the settings for the Virtual Memory from system managed size to a fixed custom size. On some computers this seems to affect their abilities of 3D-representation.

  5. In one case a user who has replaced a competing software by Delta2D reported that the 3D-Problem has been resolved by uninstalling the competing software. However, in general it will be difficult to locate the problematic software.

 

Solutions

Please ask your system administrator for help if you have insufficient rights to maintain your system or if you feel uncertain how to deal with the following suggestions.

Please note that the solutions 2 and 3 only apply to Delta2D 4.0 and newer; older versions of Delta2D are not supported any more.

1. First update your graphics drivers

This already helps in four out of five cases. Background: Delta2D is always shipped with the latest Java 3D components, which require OpenGL in a certain minimum version. For now OpenGL 1.3 has to be supported by your graphics board and its drivers.

Now Find out if and which Version of OpenGL your Computer Supports

On a windows system you can use the command line tool wglinfo, under linux you can use the in most cases already available command "glxinfo" to find out, which version of OpenGL is supported by your system. There comes quite a lot of output; simply search (linux: grep) for the string "OpenGL version string:". If this value is not something like '1.2' or '3.0.0', you can be pretty sure that OpenGL will not work. In this case you can directly jump to Using DirectDraw as replacement for OpenGL. If the version reported is lower than the version mentioned above, try the next step.

2. Downgrade the Java 3D components of your Delta2D installation to an older version.

One by one you can try out which Java3D version from the list below can work with the OpenGL version available with your graphics board. Please make sure to try them all before you give up. We already met the weirdest combinations of graphics board and J3D-versions working or not.

Replacing the Java 3D Component of Delta2D by Older Versions

The lists below offer Java 3D component installation files for Windows 32bit and 64bit, Mac and Linux 32bit and 64bit in descending version sequence. Please start testing with the topmost version matching your operating system and proceed with older versions if the tried version does not fix the problem.

  • Quit Delta2D.

  • Download the setup file to your computer.

  • For linux(32+64) only:Make the downloaded file executable: cd to the folder where the downloaded file is saved and type

    chmod u+x Delta2D_J3D_1_5_2_linux.bin

    (resp. the matching filename)

  • Execute the file by double clicking on it and follow the instructions of the setup wizard.

  • Please make sure to choose the correct installation folder of Delta2D.

  • Start Delta2D.

 

File Size
Delta2D_J3D_1_5_2_windows64.exe 4.8 MB
Delta2D_J3D_1_5_2_windows.exe 4.8 MB
Delta2D_J3D_1_5_2_mac.dmg 4.0 MB
Delta2D_J3D_1_5_2_linux64.sh 3.3 MB
Delta2D_J3D_1_5_2_linux.sh 3.3 MB

 

3. Using DirectDraw as replacement for OpenGL

With the topmost version of the Java 3D component, J3D 1.5.2, on modern Microsoft Windows systems Delta2D can use DirectX instead of OpenGL for 3D-representation. It might not look as nice as with OpenGL, but it can be helpful though. Please follow these steps:

Quit Delta2D.

  • Locate the folder of your Delta2D-installation, mostly something like "C:\Program Files\DECODON\Delta2D"
  • In the subfolder etc you can find the file called "Delta2D.conf"; open it with any editor.
  • Please append
    -J-Dj3d.rend=d3d
    at the bottom so that it looks like that:

    default_options="-J-Xms32m -J-Xmx2048M -J-XX:PermSize=32m -J-XX:MaxPermSize=128m -J-XX:+UseConcMarkSweepGC -J-XX:+CMSClassUnloadingEnabled -J-Dswing.disablevistaanimation=true -J-Dsun.java2d.d3d=false -Dj3d.rend=d3d"
  • Save the file.

Start Delta2D.

Please note:
It might be necessary to update the DirectX driver from Microsoft, too.

4. Try older versions of Java3D

If this does not help either, or with MacOS or Linux Computers, please continue trying older versions of J3D:

File Size
Delta2D_J3D_1_5_1_windows64.exe 4.6 MB
Delta2D_J3D_1_5_1_windows.exe 4.8 MB
Delta2D_J3D_1_5_1_mac.dmg 4.0 MB
Delta2D_J3D_1_5_1_linux64.sh 3.3 MB
Delta2D_J3D_1_5_1_linux.sh 3.3 MB
   
Delta2D_J3D_1_5_0_windows64.exe 4.0 MB
Delta2D_J3D_1_5_0_windows.exe 4.2 MB
Delta2D_J3D_1_5_0_mac.dmg 3.4 MB
Delta2D_J3D_1_5_0_linux64.sh 2.7 MB
Delta2D_J3D_1_5_0_linux.sh 2.7 MB
   
Delta2D_J3D_1_4_0_windows.exe 4.1 MB
Delta2D_J3D_1_4_0_linux64.sh 2.7 MB
Delta2D_J3D_1_4_0_linux.sh 2.7 MB
   
Delta2D_J3D_1_3_2_windows.exe 3.9 MB
Delta2D_J3D_1_3_2_linux64.sh 2.5 MB
Delta2D_J3D_1_3_2_linux.sh 2.5 MB

Reset the virtual memory settings in your Windows Settings to system managed size. Reboot your computer if necessary.

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